The Transportation Security Administration will remove 174 full-body scanners from airport security checkpoints, ending a $40 million contract for the machines, which caused a uproar because they revealed spectral naked forms of passengers.

TSA Administrator John Pistole issued the order this week after concluding that new software that made the machines less intrusive could not be developed by a June 1 deadline mandated by Congress.

Public outcry over heightened airport security checks, fueled by viral videos of small children being frisked and of a man warning a TSA agent, “Don’t touch my junk,” made the scanner and pat-down controversy fodder for late-night television comedians.

“It’s another very bad decision by TSA coming home to roost,” said Rep. John Mica, R-Fla., who said he will use his new role as chairman of a House Oversight subcommittee to scrutinize the agency. “It’s another disappointing chapter, and the taxpayers are going to take it on the chin.”

Mica estimated that when TSA training and the cost of replacement machines are factored in, the cost will run to “hundreds of millions of dollars.”

The machines caused a furor when they went into service in 2010 because of the revealing images they transmitted to backroom TSA surveillance personnel and because people who refused to submit to them were subject to a thorough frisking.

A vocal, infuriated minority of Americans pressured the Obama administration and Congress to find a less-intrusive method for trying to ensure air safety. Pistole was called to Capitol Hill but remained stalwart, insisting that the scanners are necessary in the defense against inventive terrorists obsessed with attacking aviation.

Most people surveyed in two 2010 polls said they agreed with Pistole: 81 percent in a CBS poll and nearly two-thirds in a Washington Post-ABC News poll.

When Pistole refused to budge, Congress appended legislation to a transportation bill requiring the TSA to develop less-revealing software for its machines.

The agency was successful in developing that for one type of scanner, the kind that looks like a glass closet and uses millimeter wave technology. Eighteen months ago, the TSA began equipping those machines with laptop-size screens that display a cookie-cutter image of the human form.

If a passenger is cleared by the scan, the screen flashes green with an “OK.” If suspicious items are detected, boxes outlined in red appear on generic front and back silhouettes to show their location.

But the agency had no success in creating similar software for 250 machines — 174 of them in service and 76 in warehouses — that use X-ray backscatter technology.

With the deadline looming and seeing little promise that the software was on track, Pistole canceled the contract in a letter delivered Thursday to Rapiscan, the Arlington, Va. company that developed the machines and was responsible for coming up with a software fix. A TSA spokesman said Rapiscan would pay for removal of the machines from airports by May 31.

The machines will be replaced with millimeter wave scanners, the spokesman said.

The backscatter machines have been banned in Europe over concerns that their radiation was a health risk for passengers. Similar concerns were raised in the United States, but they were dismissed by the TSA.

A person familiar with the machines, who has done contract work for the TSA and therefore spoke on the condition of anonymity, said the agency may harbor concerns about the radiation danger that contributed to this week’s decision.

“I suspect they may have had additional concerns that they’re not talking about,” the person said. “I believe they feel politically uncomfortable going back on their previous statements.”

Until those new machines are in place, one terrorism security expert said, the capacity of checkpoints will be diminished. The TSA said it had not determined how long it would take to have the replacement machines up and running.

“You can assume until then that you will have a reduction in security,” said Rafi Ron, a former Israeli security operative who works as a consultant in McLean, Va. “That will require a manual pat-down, which is not well accepted by the public, for good reason.”

But another leading terrorism expert said Friday that the checkpoints have only a limited impact on overall aviation security.

“Although weapons have been found and a few criminal suspects have been stopped, most of them have been people who are behind in their alimony payments,” said Richard Bloom, who has worked with U.S. intelligence agencies.

Bloom said security checkpoints may intercept mentally instable people bent on solo terrorist acts, they don’t catch terrorists such as those who pulled off the 9/11 attacks.

“If you’re talking about a sophisticated terrorist group with a sophisticated plan, these [checkpoints] have little impact,” said Bloom, who teaches at Embry-Riddle Aeronautical University. “If you know where the machines are, you just go somewhere else.”

In a written statement, the agency said, “TSA has terminated part of a contract with Rapiscan since the company is unable to deploy non-imaging Automated Target Recognition software by the Congressionally-mandated June 2013 deadline.

“By June 1, 2013 travelers will only see machines which have ATR that allow for faster throughput. This means faster lanes for the traveler and enhanced security. As always, use of this technology is optional.”